Search results for: soil-post interaction modeling

Authors: Danish Idrees, Vijay Kumar, Samudrala Gourinath

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Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1). The use of small molecules has been shown to stabilize the SOD1 dimer and preventing its dissociation and aggregation. In this study, we employed molecular docking, molecular dynamics simulation and surface plasmon resonance (SPR) to study the interactions between SOD1 and natural polyphenolic compounds. In order to explore the noncovalent interaction between SOD1 and natural polyphenolic compounds, molecular docking and molecular dynamic (MD) simulations were employed to gain insights into the binding modes and free energies of SOD1-polyphenolic compounds. MM/PBSA methods were used to calculate free energies from obtained MD trajectories. The compounds, Hesperidin, Ergosterol, and Rutin showed the excellent binding affinity in micromolar range with SOD1. Ergosterol and Hesperidin have the strongest binding affinity to SOD1 and was subjected to further characterization. Biophysical experiments using Circular Dichroism and Thioflavin T fluorescence spectroscopy results show that the binding of these two compounds can stabilize SOD1 dimer and inhibit the aggregation of SOD1. Molecular simulation results also suggest that these compounds reduce the dissociation of SOD1 dimers through direct interaction with the dimer interface. This study will be helpful to develop other drug-like molecules which may have the effect to reduce the aggregation of SOD1.

Keywords: amyotrophic lateral sclerosis, molecular dynamics simulation, surface plasmon resonance, superoxide dismutase

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Authors: Agnieszka H. Ludwig-Slomczynska, Michal T. Seweryn, Przemyslaw Kapusta, Ewelina Pitera, Katarzyna Cyganek, Urszula Mantaj, Lucja Dobrucka, Ewa Wender-Ozegowska, Maciej T. Malecki, Pawel Wolkow

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Obesity results from an imbalance between energy intake and its expenditure. Genome-Wide Association Study (GWAS) analyses have led to discovery of only about 100 variants influencing body mass index (BMI), which explain only a small portion of genetic variability. Analysis of gene epistasis gives a chance to discover another part. Since it was shown that interaction and communication between nuclear and mitochondrial genome are indispensable for normal cell function, we have looked for epistatic interactions between the two genomes to find their correlation with BMI. Methods: The analysis was performed on 366 T1DM patients using Illumina Infinium OmniExpressExome-8 chip and followed by imputation on Michigan Imputation Server. Only genes which influence mitochondrial functioning (listed in Human MitoCarta 2.0) were included in the analysis – variants of nuclear origin (MAF > 5%) in 1140 genes and 42 mitochondrial variants (MAF > 1%). Gene expression analysis was performed on GTex data. Association analysis between genetic variants and BMI was performed with the use of Linear Mixed Models as implemented in the package 'GENESIS' in R. Analysis of association between mRNA expression and BMI was performed with the use of linear models and standard significance tests in R. Results: Among variants involved in epistasis between mitochondria and nucleus we have identified one in mitochondrial transcription factor, TFB2M (rs6701836). It interacted with mitochondrial variants localized to MT-RNR1 (p=0.0004, MAF=15%), MT-ND2 (p=0.07, MAF=5%) and MT-ND4 (p=0.01, MAF=1.1%). Analysis of the interaction between nuclear variant rs6701836 (nuc) and rs3021088 localized to MT-ND2 mitochondrial gene (mito) has shown that the combination of the two led to BMI decrease (p=0.024). Each of the variants on its own does not correlate with higher BMI [p(nuc)=0.856, p(mito)=0.116)]. Although rs6701836 is intronic, it influences gene expression in the thyroid (p=0.000037). rs3021088 is a missense variant that leads to alanine to threonine substitution in the MT-ND2 gene which belongs to complex I of the electron transport chain. The analysis of the influence of genetic variants on gene expression has confirmed the trend explained above – the interaction of the two genes leads to BMI decrease (p=0.0308). Each of the mRNAs on its own is associated with higher BMI (p(mito)=0.0244 and p(nuc)=0.0269). Conclusıons: Our results show that nuclear-mitochondrial epistasis can influence BMI in T1DM patients. The correlation between transcription factor expression and mitochondrial genetic variants will be subject to further analysis.

Keywords: body mass index, epistasis, mitochondria, type 1 diabetes

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Authors: Sarra Zaied, Arthur Bonpain, Pierre Yves Fravallo

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The permanent supply of marine litter implies their accumulation in the oceans, which causes the presence of more compact wastes layers. Their Spatio-temporal distribution is never homogeneous and depends mainly on the hydrodynamic characteristics of the environment and the size and location of the wastes. As part of optimizing collect of marine plastic wastes, it is important to measure and monitor their evolution over time. For this, many research studies have been dedicated to describing the wastes behavior in order to identify their accumulation in oceans areas. Several models are therefore developed to understand the mechanisms that allow the accumulation and the displacements of marine litter. These models are able to accurately simulate the drift of wastes to study their behavior and stranding. However, these works aim to study the wastes behavior over a long period of time and not at the time of waste collection. This work investigates the transport of floating marine litter (FML) to provide basic information that can help in optimizing wastes collection by proposing a model for predicting their behavior during collection. The proposed study is based on a Lagrangian modeling approach that uses the main factors influencing the dynamics of the waste. The performance of the proposed method was assessed on real data collected from the Copernicus Marine Environment Monitoring Service (CMEMS). Evaluation results in the Java Sea (Indonesia) prove that the proposed model can effectively predict the position and the velocity of marine wastes during collection.

Keywords: floating marine litter, lagrangian transport, particle-tracking model, wastes drift

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Authors: Bello Gonzalez, Setten Van M., Brouwer M.

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The chicken small intestine represents a dynamic and complex organ in which the enzymatic digestion and absorption of nutrients take place. The development of an in vitro fermentation chicken small intestinal model could be used as an alternative to explore the interaction between the microbiota and nutrient metabolism and to enhance the efficacy of targeting interventions to improve animal health. In the present study we have developed an in vitro fermentation chicken ileum microbiota model for unrevealing the complex interaction of ileum microbial community under physiological conditions. A two-vessel continuous fermentation process simulating in real-time the physiological conditions of the ileum content (pH, temperature, microaerophilic/anoxic conditions, and peristaltic movements) has been standardized as a proof of concept. As inoculum, we use a pool of ileum microbial community obtained from chicken broilers at the age of day 14. The development and validation of the model provide insight into the initial characterization of the ileum microbial community and its dynamics over time-related to nutrient assimilation and fermentation. Samples can be collected at different time points and can be used to determine the microbial compositional structure, dynamics, and diversity over time. The results of studies using this in vitro model will serve as the foundation for the development of a whole small intestine in vitro fermentation chicken gastrointestinal model to complement our already established in vitro fermentation chicken caeca model. The insight gained from this model could provide us with some information about the nutritional strategies to restore and maintain chicken gut homeostasis. Moreover, the in vitro fermentation model will also allow us to study relationships between gut microbiota composition and its dynamics over time associated with nutrients, antimicrobial compounds, and disease modelling.

Keywords: broilers, in vitro model, ileum microbiota, fermentation

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Authors: Mohamed Eltarabily, Abdelazim Negm, Chihiro Yoshimura

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Recently, the pollution of groundwater from the use of nitrogenous fertilizer is at the increase. Also, due to the increase in area under cultivation and regular use of fertilizer in irrigated agriculture, groundwater pollution from agricultural activities is becoming a major concern. Because of the high mobility of Nitrate (NO3-) in soil which is governed by electrostatic processes, particularly anion exclusion, nitrate can be intercepted by shallow subsurface drainage pipe systems and then discharged offsite into streams, rivers, and lakes causing many hazards. In order to solve these environmental problems associated with nitrate, a better understanding of how NO3- moves through the soil profile under flow conditions is required. In the present paper, the results of a comparative study between experimental and numerical modeling of Nitrate transport through a saturated soil column are presented and analyzed. In order to achieve that, three water fluxes densities; 0.008, 0.007, and 0.006 m sec-1 and N concentration rates 10 mol cm-3 were used. The same concentrations were used in the simulation using HYDRUS-2D. The physical and chemical properties of the collected soil samples were calculated. Besides, the soil texture was determined which was silty sand. Results showed that HYDRUS-2D can successfully predict the relative behavior of N transport in the present experiment. Nitrate concentrations will reach deeper depth with the increase in the water flux. Overall, it was overestimated in the final concentration of (NO3-) in the soil by numerical simulation than by experimental column test. The column experiment is a useful tool for assessing the nitrate concentrations in the soil profile.

Keywords: groundwater, nitrate leaching, HYDRUS-2D, soil column

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Authors: Carla Maria Furuno Rimkus

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The technologies related to virtual reality and augmented reality in combination with mobile technologies, are being more consolidated and used each day. The increasing technological availability along with the decrease of their acquisition and maintenance costs, have favored the expansion of its use in the field of historic heritage. In this context it is focused, in this article, on the potential of mobile applications in the dissemination of the architectural heritage, using the technology of Augmented Reality. From this perspective approach, it is discussed about the process of producing an application for mobile devices on the Android platform, which combines the technologies of geometric modeling with augmented reality (AR) and access to interactive multimedia contents with cultural, social and historic information of the historic building that we take as the object of study: a block with a set of buildings built in the XVIII century, known as "Quarteirão dos Trapiches", which was modeled in 3D, coated with the original texture of its facades and displayed on AR. From this perspective approach, this paper discusses about methodological aspects of the development of this application regarding to the process and the project development tools, and presents our considerations on methodological aspects of developing an application for the Android system, focused on the dissemination of the architectural heritage, in order to encourage the tourist potential of the city in a sustainable way and to contribute to develop the digital documentation of the heritage of the city, meeting a demand of tourists visiting the city and the professionals who work in the preservation and restoration of it, consisting of architects, historians, archaeologists, museum specialists, among others.

Keywords: augmented reality, architectural heritage, geometric modeling, mobile applications

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Authors: Mayank, Navneet Kaur, Narinder Singh

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The V599 mutations in the BRAF protein are extremely oncogenic, responsible for countless of malignant conditions. Along with wild type, V599E, V599D, and V599R are the important mutated variants of the BRAF proteins. The BRAF inhibitory anticancer agents are continuously developing, and sorafenib is a BRAF inhibitor that is under clinical use. The crystal structure of sorafenib bounded to wild type, and V599 is known, showing a similar interaction pattern in both the case. The mutated 599th residue, in both the case, is also found not interacting directly with the co-crystallized sorafenib molecule. However, the IC50 value of sorafenib was found extremely different in both the case, i.e., 22 nmol/L for wild and 38 nmol/L for V599E protein. Molecular docking study and MMGBSA binding energy results also revealed a significant difference in the binding pattern of sorafenib in both the case. Therefore, to explore the role of distinctively situated 599th residue, we have further conducted comprehensive computational studies. The molecular dynamics simulation, residue interaction network (RIN) analysis, and residue correlation study results revealed the importance of the 599th residue on the therapeutic outcome and overall dynamic of the BRAF protein. Therefore, although the position of 599th residue is very much distinctive from the ligand-binding cavity of BRAF, still it has exceptional control over the overall functional outcome of the protein. The insight obtained here may seem extremely important and guide us while designing ideal BRAF inhibitory anticancer molecules.

Keywords: BRAF, oncogenic, sorafenib, computational studies

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Authors: Claudia García-García, Catalina B. García-García, Román Salmerón-Gómez

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Much economic-environmental research includes the analysis of possible interactions by using Moderated Regression Analysis (MRA), which is a specific application of multiple linear regression analysis. This methodology allows analyzing how the effect of one of the independent variables is moderated by a second independent variable by adding a cross-product term between them as an additional explanatory variable. Due to the very specification of the methodology, the moderated factor is often highly correlated with the constitutive terms. Thus, great multicollinearity problems arise. The appearance of strong multicollinearity in a model has important consequences. Inflated variances of the estimators may appear, there is a tendency to consider non-significant regressors that they probably are together with a very high coefficient of determination, incorrect signs of our coefficients may appear and also the high sensibility of the results to small changes in the dataset. Finally, the high relationship among explanatory variables implies difficulties in fixing the individual effects of each one on the model under study. These consequences shifted to the moderated analysis may imply that it is not worth including an interaction term that may be distorting the model. Thus, it is important to manage the problem with some methodology that allows for obtaining reliable results. After a review of those works that applied the MRA among the ten top journals of the field, it is clear that multicollinearity is mostly disregarded. Less than 15% of the reviewed works take into account potential multicollinearity problems. To overcome the issue, this work studies the possible application of recent methodologies to MRA. Particularly, the raised regression is analyzed. This methodology mitigates collinearity from a geometrical point of view: the collinearity problem arises because the variables under study are very close geometrically, so by separating both variables, the problem can be mitigated. Raise regression maintains the available information and modifies the problematic variables instead of deleting variables, for example. Furthermore, the global characteristics of the initial model are also maintained (sum of squared residuals, estimated variance, coefficient of determination, global significance test and prediction). The proposal is implemented to data from countries of the European Union during the last year available regarding greenhouse gas emissions, per capita GDP and a dummy variable that represents the topography of the country. The use of a dummy variable as the moderator is a special variant of MRA, sometimes called “subgroup regression analysis.” The main conclusion of this work is that applying new techniques to the field can improve in a substantial way the results of the analysis. Particularly, the use of raised regression mitigates great multicollinearity problems, so the researcher is able to rely on the interaction term when interpreting the results of a particular study.

Keywords: multicollinearity, MRA, interaction, raise

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Authors: Emma Avoyan

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The safety standards for flood protection in the Netherlands have been revised recently. It is expected that all major flood-protection structures will have to be reinforced to meet the new standards. The Dutch Flood Protection Programme aims at accomplishing this task through innovative integrated projects such as construction of multi-functional flood defenses. In these projects, flood safety purposes will be combined with spatial planning, nature development, emergency management or other sectoral objectives. Therefore, implementation of dike reinforcement projects requires early involvement and collaboration between public and private sectors, different governmental actors and agencies. The development and implementation of such integrated projects has been an issue in Dutch flood risk management since long. Therefore, this article analyses how cross-sector collaboration within flood risk governance in the Netherlands has evolved over time, and how this development can be explained. The integrative framework for collaborative governance is applied as an analytical tool to map external factors framing possibilities as well as constraints for cross-sector collaboration in Dutch flood risk domain. Supported by an extensive document and literature analysis, the paper offers insights on how the system context and different drivers changing over time either promoted or hindered cross-sector collaboration between flood protection sector, urban development, nature conservation or any other sector involved in flood risk governance. The system context refers to the multi-layered and interrelated suite of conditions that influence the formation and performance of complex governance systems, such as collaborative governance regimes, whereas the drivers initiate and enable the overall process of collaboration. In addition, by applying a method of process tracing we identify a causal and chronological chain of events shaping cross-sectoral interaction in Dutch flood risk management. Our results indicate that in order to evaluate the performance of complex governance systems, it is important to firstly study the system context that shapes it. Clear understanding of the system conditions and drivers for collaboration gives insight into the possibilities of and constraints for effective performance of complex governance systems. The performance of the governance system is affected by the system conditions, while at the same time the governance system can also change the system conditions. Our results show that the sequence of changes within the system conditions and drivers over time affect how cross-sector interaction in Dutch flood risk governance system happens now. Moreover, we have traced the potential of this governance system to shape and change the system context.

Keywords: collaborative governance, cross-sector interaction, flood risk management, the Netherlands

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Authors: Eszter J. Tóth, Alexandra Hoffmann, Csaba Vágvölgyi, Tamás Papp

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Members of the genera Curvularia and Bipolaris are closely related melanin producing filamentous fungi; both of them have the teleomorph states in genus Cochliobolus. While Bipolaris species infect only plants and may cause serious agriculture damages, some Curvularia species was recovered from opportunistic human infections. The human pathogenic species typically cause phaeohyphomycoses, i.e. mould infections caused by melanised fungi, which can manifest as invasive mycoses with frequent involvement of the central nervous system in immunocompromised patients or as local infections (e.g. keratitis, sinusitis, and cutaneous lesions) in immunocompetent people. Although their plant-fungal interactions have been intensively studied, there is only little information available about the human pathogenic feature of these fungi. The aim of this study was to investigate the neutrophil granulocytes’ response to hyphal forms of Curvularia and Bipolaris in comparison with the response to Aspergillus. In the present study Curvularia lunata SZMC 23759 and Aspergillus fumigatus SZMC 23245 both isolated from human eye infection, and Bipolaris zeicola BRIP 19582b isolated from plant leaf were examined. Neutrophils were isolated from heparinised venous blood of healthy donors with dextran sedimentation followed by centrifugation over Ficoll and hypotonic lysis of erythrocytes. Viability and purity of the cells were checked with trypan blue and Wright staining, respectively. Infection of neutrophils was carried out with germinated conidia in a ratio of 5:1. Production of hydrogen peroxide, superoxide anion, and nitrogen monoxide was measured both intracellularly and extracellularly in response to the germinated spores with or without the supernatant and after serum treatment. ROS and NOS production of neutrophils in interaction with the three fungi were compared. It is already known that Aspergillus species induce ROS production of neutrophils only after serum treatment. Although, in case of C. lunata, serum opsonisation also induced an intensive production of reactive species, lower level of production was measured in the lack of serum as well. After interaction with the plant pathogenic B. zeicola, amount of reactive species found to be similar with and without serum treatment. The presence of germination supernatant decreased the reactive species production in case of each fungus. Interaction with Curvularia, Bipolaris and Aspergillus species induced different response of neutrophils. It seems that recognition of C. lunata and B. zeicola is independent of serum opsonisation, albeit it increases the level of the produced reactive species in response for C. lunata. The study was supported by the grant LP2016-8/2016.

Keywords: Curvularia, neutrophils, NOS, ROS, serum opsonisation

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Authors: Antonis Elia, Theo Loizou, Gladys Onambele-Pearson, Matthew Barlow, Georgina Stebbings

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Hypoxic conditions have been reported to enhance red blood cell production in both acclimatised low-landers and altitude adapted populations. This process is mediated by the erythropoietin hormone, which is released predominantly by the hypoxic kidney. A higher haemoglobin concentration was previously reported in elite breath-hold divers when compared to elite-skiers and untrained individuals. Therefore, the present study aimed to investigate whether apnoea induced hypoxia could induce a significant increase in serum erythropoietin concentration in recreational breath-hold divers which would provide an explanation to the higher haemoglobin levels observed in elite breath-hold divers. Identifying whether apnoea induced hypoxia induces a significant increase in serum erythropoietin might suggest that apnoea can be used as an alternative acclimatisation method to high altitude exposure. Seven healthy, recreational male breath-hold divers performed two sets of five 180 second breath-holds with a ten-minute supine rest between each set and a two-minute seated rest between each apnoea. During each breath-hold, participant’s heart rate and peripheral oxygen saturation levels were recorded every subsequent 10 seconds until the end of the 180 second breath-hold. After each 180 second breath-hold a capillary blood sample was collected from the finger to identify circulating haemoglobin levels. Following completion of the apnoeic protocol, three blood samples were collected at 30, 90 and 180 minutes to measure circulating erythropoietin levels. A significant interaction between erythropoietin and time was observed (F(3,18)= 4.72, p < 0.001), with significant increases in erythropoietin evident at 30 (t(6)= -5.035, p < 0.0590 (t(6)= -6.162, p < 0.05) and 180 (t(6)= - 7.232, p < 0.001) minutes post the last apnoea when compared to baseline. Corresponding average increases when compared to baseline were 16% at 30, 23% at 90 and 40% at 180 minutes post the last apnoea. A significant interaction between haemoglobin and time was observed (F(78,84)= 20.814, p < 0.001), with significant increases in haemoglobin evident at the fifth (t(29)= -1.124, p < 0.001), ninth (t(29)= -1.357, p < 0.001) and tenth (t(29)= -1.211, p < 0.05) apnoeas when compared to baseline. A significant interaction between peripheral oxygen saturation and time was observed (F(10,60)= 408.23, p < 0.001). The present study demonstrates that a series of ten 180 second breath-holds is sufficient to induce a significant increase in the circulating erythropoietin concentration of recreational breath hold divers. These observations may suggest that apnoea induced hypoxia may be used as an alternative acclimatisation method to high altitude exposure.

Keywords: apnoea, breath-holding, diving reflex, erythropoietin, haemoglobin

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Authors: Tamer M. Shehata, Heba S. Elsewedy, Mashel Al Dosary, Alaa Elshehry, Mohamed A. Khedr, Maged E. Mohamed

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Objective: 2,4-Dichlorophenoxy acetic acid (2,4-D) is a well-known herbicide widely used as a weed killer. Recently, 2,4-D was rediscovered as a new anti-inflammatory agent through in silico as well as in-vivo experiments. However, poor solubility of 2,4-D could represent a problems during pharmaceutical development in addition to lower bioavailability. Solid dispersion (SD) refers to a group of solid products consisting of at least two different components, usually a hydrophobic drug and hydrophilic matrix. It is well known technique for enhancing drug solubility. Therefore, selecting SD as a tool for enhancing 2,4-D could be of great interest to the formulator. Method: In our project, several polymers were investigated (such as PEG, HPMC, citric acid and others) in addition to drug polymer ratios and its effect on solubility. Evaluation of drug polymer interaction was investigated through both Fourier Transform Infrared (FTIR) and Differential Scanning Calorimetry (DSC). Finally, in-vivo evaluation was performed for the best selected preparation through inflammatory response of rat induce hind paw. Results: Results indicated that, citric acid 2,4-D and in ratio of 0.75 : 1 showed modified the dissolution profile of the drug. The FTIR resltes indicated no significant chemical interaction, however DSC showed shifting of the drug melting point. Finally, Carragenan induced rat hind paw edema showed significant reduction of the drug solid dispersion in comparison to the pure drug, indicating rapid and complete absorption of the drug in solid dispersion form. Conclusion: Solid dispersion technology can be utilized efficiently to enhance the solubility of 2,4-D.

Keywords: solid dispersion, 2, 4-D solubility, carragenan induced edema

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Authors: I. Yordanova, H. Kolev, S. Todorova, Z. Cherkezova-Zheleva

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Catalysis plays a key role in solving many environmental problems by establishing efficient catalytic systems for environmental protection and reducing emissions of greenhouse gases from industry. Volatile organic compounds are major air pollutants. There are several ways to dispose of emissions like - adsorption, condensation, absorption, bio-filtration, thermal, catalytic, plasma and ultraviolet oxidation. The catalytic oxidation has more advantages over other methods. For example - lower energy consumption; the concentration of the organic contaminant may be low or may vary within wide limits. Catalysts for complete oxidation of VOCs can be classified into three categories: noble metal, metal oxides or supported metal oxides and mixture of noble metals and metal oxides. Most of the catalysts for the complete catalytic oxidation are based on Pt, Pd, Rh or a combination thereof. The oxides of the transition metal are one of the alternatives to noble metal catalysts for these reactions. They are less active at low temperatures, but at higher - their activity is similar. The properties of the catalyst depend on the distribution of the active phase, the medium type of the pre-treatment, the interaction between the active phase and the support and the interaction between the active phase and the reaction medium. Supported mono-component Mn and bi-component Mn-Co systems are examined in present study. The samples are prepared using co-precipitation method. SiO2 (Aerosil) is used as a support. The studied samples were precipitated by NH4OH. The synthesized samples were characterized by XRD, XPS, TPR and tested in the catalytic reaction of complete oxidation of n-hexane, propane, methanol, ethanol and propanol.

Keywords: catalytic oxidation, Co-Mn oxide, oxidation of hydrocarbons and alcohols, environmental protection

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Authors: Julia Desiree Velastegui Caceres, Luis Alejandro Velastegui Caceres, Oswaldo Padilla, Eduardo Kirby, Francisco Guerrero, Theofilos Toulkeridis

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It is fundamental to conserve sites of natural and cultural heritage with any available technique or existing methodology of preservation in order to sustain them for the following generations. We propose a further skill to protect the actual view of such sites, in which with high technology instrumentation we are able to digitally preserve natural and cultural heritages applied in Ecuador. In this project the use of laser technology is presented for three-dimensional models, with high accuracy in a relatively short period of time. In Ecuador so far, there are not any records on the use and processing of data obtained by this new technological trend. The importance of the project is the description of the methodology of the laser scanner system using the Faro Laser Scanner Focus 3D 120, the method for 3D modeling of geospatial data and the development of virtual environments in the areas of Cultural and Natural Heritage. In order to inform users this trend in technology in which three-dimensional models are generated, the use of such tools has been developed to be able to be displayed in all kinds of digitally formats. The results of the obtained 3D models allows to demonstrate that this technology is extremely useful in these areas, but also indicating that each data campaign needs an individual slightly different proceeding starting with the data capture and processing to obtain finally the chosen virtual environments.

Keywords: laser scanner system, 3D model, cultural heritage, natural heritage

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Authors: Chansheng He, Zhongfu Wang, Xiao Bai, Jie Tian, Xin Jin

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Heterogeneity of soil hydraulic properties directly affects hydrological processes at different scales. Understanding heterogeneity of soil hydraulic properties such as soil moisture is therefore essential for modeling watershed ecohydrological processes, particularly in hard to access, topographically complex mountainous watersheds. This study maps spatial variations of soil moisture by in situ observation network that consists of sampling points, zones, and tributaries, and monitors corresponding hydrological variables of air and soil temperatures, evapotranspiration, infiltration, and runoff in the Upper Reach of the Heihe River Watershed, a second largest inland river (terminal lake) with a drainage area of over 128,000 km² in Northwest China. Subsequently, the study uses a hydrological model, SWAT (Soil and Water Assessment Tool) to simulate the effects of heterogeneity of soil moisture on watershed hydrological processes. The spatial clustering method, Full-Order-CLK was employed to derive five soil heterogeneous zones (Configuration 97, 80, 65, 40, and 20) for soil input to SWAT. Results show the simulations by the SWAT model with the spatially clustered soil hydraulic information from the field sampling data had much better representation of the soil heterogeneity and more accurate performance than the model using the average soil property values for each soil type derived from the coarse soil datasets. Thus, incorporating detailed field sampling soil heterogeneity data greatly improves performance in hydrologic modeling.

Keywords: heterogeneity, soil moisture, SWAT, up-scaling

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Authors: Abimbola M. Enitan, J. Adeyemo

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Anaerobic modeling is a useful tool to describe and simulate the condition and behaviour of anaerobic treatment units for better effluent quality and biogas generation. The present investigation deals with the anaerobic treatment of brewery wastewater with varying organic loads. The chemical oxygen demand (COD) and total suspended solids (TSS) of the influent and effluent of the bioreactor were determined at various retention times to generate data for kinetic coefficients. The bio-kinetic coefficients in the modified Stover–Kincannon kinetic and methane generation models were determined to study the performance of anaerobic digestion process. At steady-state, the determination of the kinetic coefficient (K), the endogenous decay coefficient (Kd), the maximum growth rate of microorganisms (µmax), the growth yield coefficient (Y), ultimate methane yield (Bo), maximum utilization rate constant Umax and the saturation constant (KB) in the model were calculated to be 0.046 g/g COD, 0.083 (dˉ¹), 0.117 (d-¹), 0.357 g/g, 0.516 (L CH4/gCODadded), 18.51 (g/L/day) and 13.64 (g/L/day) respectively. The outcome of this study will help in simulation of anaerobic model to predict usable methane and good effluent quality during the treatment of industrial wastewater. Thus, this will protect the environment, conserve natural resources, saves time and reduce cost incur by the industries for the discharge of untreated or partially treated wastewater. It will also contribute to a sustainable long-term clean development mechanism for the optimization of the methane produced from anaerobic degradation of waste in a close system.

Keywords: brewery wastewater, methane generation model, environment, anaerobic modeling

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Authors: Oleg Reva, Ilya Korotetskiy, Marina Lankina, Murat Kulmanov, Aleksandr Ilin

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Molecular docking approaches are widely used for design of new antibiotics and modeling of antibacterial activities of numerous ligands which bind specifically to active centers of indispensable enzymes and/or key signaling proteins of pathogens. Widespread drug resistance among pathogenic microorganisms calls for development of new antibiotics specifically targeting important metabolic and information pathways. A generally recognized problem is that almost all molecular targets have been identified already and it is getting more and more difficult to design innovative antibacterial compounds to combat the drug resistance. A promising way to overcome the drug resistance problem is an induction of reversion of drug resistance by supplementary medicines to improve the efficacy of the conventional antibiotics. In contrast to well established computer-based drug design, modeling of drug resistance reversion still is in its infancy. In this work, we proposed an approach to identification of compensatory genetic variants reducing the fitness cost associated with the acquisition of drug resistance by pathogenic bacteria. The approach was based on an analysis of the population genetic of Mycobacterium tuberculosis and on results of experimental modeling of the drug resistance reversion induced by a new anti-tuberculosis drug FS-1. The latter drug is an iodine-containing nanomolecular complex that passed clinical trials and was admitted as a new medicine against MDR-TB in Kazakhstan. Isolates of M. tuberculosis obtained on different stages of the clinical trials and also from laboratory animals infected with MDR-TB strain were characterized by antibiotic resistance, and their genomes were sequenced by the paired-end Illumina HiSeq 2000 technology. A steady increase in sensitivity to conventional anti-tuberculosis antibiotics in series of isolated treated with FS-1 was registered despite the fact that the canonical drug resistance mutations identified in the genomes of these isolates remained intact. It was hypothesized that the drug resistance phenotype in M. tuberculosis requires an adjustment of activities of many genes to compensate the fitness cost of the drug resistance mutations. FS-1 cased an aggravation of the fitness cost and removal of the drug-resistant variants of M. tuberculosis from the population. This process caused a significant increase in genetic heterogeneity of the Mtb population that was not observed in the positive and negative controls (infected laboratory animals left untreated and treated solely with the antibiotics). A large-scale search for linkage disequilibrium associations between the drug resistance mutations and genetic variants in other genomic loci allowed identification of target proteins, which could be influenced by supplementary drugs to increase the fitness cost of the drug resistance and deprive the drug-resistant bacterial variants of their competitiveness in the population. The approach will be used to improve the efficacy of FS-1 and also for computer-based design of new drugs to combat drug-resistant infections.

Keywords: complete genome sequencing, computational modeling, drug resistance reversion, Mycobacterium tuberculosis

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Authors: Jim J. Catina, Jackee M. Gwynn, Jin S. Kang

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Additive manufacturing (AM) for hybrid rocket engines is becoming increasingly attractive due to its ability to create complex grain configurations with improved regression rates when compared to cast grains. However, the presence of microvoids in parts produced through the additive manufacturing method of Fused Deposition Modeling (FDM) results in a lower fuel density and is believed to cause a decrease in regression rate compared to ideal performance. In this experiment, FDM was used to create hybrid rocket fuel grains with a star configuration composed of acrylonitrile butadiene styrene (ABS). Testing was completed to determine the effect of heat treatment as a post-processing method to improve the combustion performance of hybrid rocket fuel grains manufactured by FDM. For control, three ABS star configuration grains were printed using FDM and hot fired using gaseous oxygen (GOX) as the oxidizer. Parameters such as thrust and mass flow rate were measured. Three identical grains were then heat treated to varying degrees and hot fired under the same conditions as the control grains. This paper will quantitatively describe the amount of improvement in engine performance as a result of heat treatment of the AM hybrid fuel grain. Engine performance is measured in this paper by specific impulse, which is determined from the thrust measurements collected in testing.

Keywords: acrylonitrile butadiene styrene, additive manufacturing, fused deposition modeling, heat treatment

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Authors: T. Yu, L. Audibert, J. F. Chaix, D. Komatitsch, V. Garnier, J. M. Henault

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Linear Ultrasonic Techniques play a major role in Non-Destructive Evaluation (NDE) for civil engineering structures in concrete since they can meet operational requirements. Interpretation of ultrasonic measurements could be improved by a better understanding of ultrasonic wave propagation in a multiple scattering medium. This work aims to develop a 2D numerical model of ultrasonic wave propagation in a heterogeneous medium, like concrete, integrating the multiple scattering phenomena in SPECFEM software. The coherent field of multiple scattering is obtained by averaging numerical wave fields, and it is used to determine the effective phase velocity and attenuation corresponding to an equivalent homogeneous medium. First, this model is applied to one scattering element (a cylinder) in a homogenous medium in a linear-elastic system, and its validation is completed thanks to the comparison with analytical solution. Then, some cases of multiple scattering by a set of randomly located cylinders or polygons are simulated to perform parametric studies on the influence of frequency and scatterer size, concentration, and shape. Also, the effective properties are compared with the predictions of Waterman-Truell model to verify its validity. Finally, the mortar viscoelastic behavior is introduced in the simulation in order to considerer the dispersion and the attenuation due to porosity included in the cement paste. In the future, different steps will be developed: The comparisons with experimental results, the interpretation of NDE measurements, and the optimization of NDE parameters before an auscultation.

Keywords: attenuation, multiple-scattering medium, numerical modeling, phase velocity, ultrasonic measurements

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Authors: Walid Tawfik

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The interaction of high intensity ultrashort laser pulses with plasma generates many significant applications, including soft x-ray lasers, time-resolved laser induced plasma spectroscopy LIPS, and laser-driven accelerators. The development in producing of femtosecond down to ten femtosecond optical pulses has facilitates scientists with a vital tool in a variety of ultrashort phenomena, such as high field physics, femtochemistry and high harmonic generation HHG. In this research, we generate a two-octave-wide ultrashort supercontinuum pulses with an optical spectrum extending from 3.5 eV (ultraviolet) to 1.3 eV (near-infrared) using a capillary fiber filled with neon gas. These pulses are formed according to nonlinear self-phase modulation in the neon gas as a nonlinear medium. The investigations of the created pulses were made using spectral phase interferometry for direct electric-field reconstruction (SPIDER). A complete description of the output pulses was considered. The observed characterization of the produced pulses includes the beam profile, the pulse width, and the spectral bandwidth. After reaching optimization conditions, the intensity of the reconstructed pulse autocorrelation function was applied for the shorts pulse duration to achieve transform limited ultrashort pulses with durations below 6-fs energies up to 600μJ. Moreover, the effect of neon pressure variation on the pulse width was examined. The nonlinear self-phase modulation realized to be increased with the pressure of the neon gas. The observed results may lead to an advanced method to control and monitor ultrashort transit interaction in femtochemistry.

Keywords: supercontinuum, ultrafast, SPIDER, ultra-broadband

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Authors: Behzad Hajalilou, Nasim Hajalilou, Saeid Ansari

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The study area is located in East Azerbaijan province, north of Ahar city, and 1/100000 geological map of Varzgan. This region is located in the middle of Iran zone. Ali Javad Porphyry copper-gold ore deposit has been created in a magmatic complex containing intrusive masses, combining Granodiorite and quartz Monzonite that penetrates into the Eocene volcanic aggregate. The most important mineralization includes primary oxides minerals (magnetite), sulfide (pyrite, chalcopyrite, Molybdenite, Bornite, Chalcocite, Covollite), secondary oxide or hydroxide minerals (hematite, goethite, limonite), and carbonate (malachite and Azurite). The mineralization forms into the vein-veinlets and scattered system. The alterations observed in the region include intermediate Argillic, advanced Argillic, Phyllic, silica, Propylitic, chlorite and Potassic. The 3D model of mineralization of the Alijavad is provided by Data DATAMINE software and based on the study of 700 polished sections of 32 drilled boreholes in the region. This model is completely compatible with the model provided by Lowell and Gilbert for the mineralization of porphyry copper deposits of quartz Monzonite type. The estimated cumulative residual value of copper for Ali Javad deposit is 81.5 million tons with 0.75 percent of copper, and for gold is 8.37 million tons with 1.8 ppm.

Keywords: porphyry copper, mineralization, Ali Javad, modeling, reserve estimation

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Authors: Martin Kittel, Alexander Roth

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The continuous integration of variable renewable energy sources (VRE) in the power sector is required for decarbonizing the European economy. Power sectors become increasingly exposed to weather variability, as the availability of VRE, i.e., mainly wind and solar photovoltaic, is not persistent. Extreme events, e.g., long-lasting periods of scarce VRE availability (‘VRE droughts’), challenge the reliability of supply. Properly accounting for the severity of VRE droughts is crucial for designing a resilient renewable European power sector. Energy system modeling is used to identify such a design. Our analysis reveals the sensitivity of the optimal design of the European power sector towards VRE droughts. We analyze how VRE droughts impact optimal power sector investments, especially in generation and flexibility capacity. We draw upon work that systematically identifies VRE drought patterns in Europe in terms of frequency, duration, and seasonality, as well as the cross-regional and cross-technological correlation of most extreme drought periods. Based on their analysis, the authors provide a selection of relevant historical weather years representing different grades of VRE drought severity. These weather years will serve as input for the capacity expansion model for the European power sector used in this analysis (DIETER). We additionally conduct robustness checks varying policy-relevant assumptions on capacity expansion limits, interconnections, and level of sector coupling. Preliminary results illustrate how an imprudent selection of weather years may cause underestimating the severity of VRE droughts, flawing modeling insights concerning the need for flexibility. Sub-optimal European power sector designs vulnerable to extreme weather can result. Using relevant weather years that appropriately represent extreme weather events, our analysis identifies a resilient design of the European power sector. Although the scope of this work is limited to the European power sector, we are confident that our insights apply to other regions of the world with similar weather patterns. Many energy system studies still rely on one or a limited number of sometimes arbitrarily chosen weather years. We argue that the deliberate selection of relevant weather years is imperative for robust modeling results.

Keywords: energy systems, numerical optimization, variable renewable energy sources, energy drought, flexibility

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Authors: Maxime Alex Junior Kuitche, Ruxandra Mihaela Botez, Jean-Chirstophe Maunand

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The evolution of aircraft is closely linked to the study and improvement of propulsion systems. Determining the propulsion performance is a real challenge in aircraft modeling and design. In addition to theoretical methodologies, experimental procedures are used to obtain a good estimation of the propulsion performances. For piston-propeller propulsion, the propeller needs several experimental tests which could be extremely demanding in terms of time and money. This paper presents a new procedure to estimate the performance of a propeller from a numerical approach using computational fluid dynamic analysis. The propeller was initially scanned, and then, its 3D model was represented using CATIA. A structured meshing and Shear Stress Transition k-ω turbulence model were applied to describe accurately the flow pattern around the propeller. Thus, the Partial Differential Equations were solved using ANSYS FLUENT software. The method was applied on the UAS-S45’s propeller designed and manufactured by Hydra Technologies in Mexico. An extensive investigation was performed for several flight conditions in terms of altitudes and airspeeds with the aim to determine thrust coefficients, power coefficients and efficiency of the propeller. The Computational Fluid Dynamics results were compared with experimental data acquired from wind tunnel tests performed at the LARCASE Price-Paidoussis wind tunnel. The results of this comparison have demonstrated that our approach was highly accurate.

Keywords: CFD analysis, propeller performance, unmanned aerial system propeller, UAS-S45

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Authors: Priscilla Echeverria

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This paper addresses initial teacher formation as a formative space in which pedagogy students develop a pedagogical agency capacity to contribute to social justice, considering ethical, political, and epistemic dimensions. This paper is structured by discussing first the concepts of agency, pedagogical interaction, and social justice from a critical perspective; and continues offering preliminary results on the capacity of pedagogical agency in novice teachers after the analysis of critical incidents as a research methodology. This study is motivated by the concern that responding to the current neoliberal scenario, many initial teacher formation (ITF) programs have reduced the meaning of education to instruction, and pedagogy to methodology, favouring the formation of a technical professional over a reflective or critical one. From this concern, this study proposes that the restitution of the subject is an urgent task in teacher formation, so it is essential to enable him in his capacity for action and advance in eliminating institutionalized oppression insofar as it affects that capacity. Given that oppression takes place in human interaction, through this work, I propose that initial teacher formation develops sensitivity and educates the gaze to identify oppression and take action against it, both in pedagogical interactions -which configure political, ethical, and epistemic subjectivities- as in the hidden and official curriculum. All this from the premise that modelling democratic and dialogical interactions are basic for any program that seeks to contribute to a more just and empowered society. The contribution of this study lies in the fact that it opens a discussion in an area about which we know little: the impact of the type of interactions offered by university teaching at ITF on the capacity of future teachers to be pedagogical agents. For this reason, this study seeks to gather evidence of the result of this formation, analysing the capacity of pedagogical agency of novice teachers, or, in other words, how capable the graduates of secondary pedagogies are in their first pedagogical experiences to act and make decisions putting the formative purposes that they are capable of autonomously defining before technical or bureaucratic issues imposed by the curriculum or the official culture. This discussion is part of my doctoral research, "The importance of developing the capacity for ethical-political-epistemic agency in novice teachers during initial teacher formation to contribute to social justice", which I am currently developing in the Educational Research program of the University of Lancaster, United Kingdom, as a Conicyt fellow for the 2019 cohort.

Keywords: initial teacher formation, pedagogical agency, pedagogical interaction, social justice, hidden curriculum

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Authors: Florin Leon, Silvia Curteanu

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Developing complete mechanistic models for polymerization reactors is not easy, because complex reactions occur simultaneously; there is a large number of kinetic parameters involved and sometimes the chemical and physical phenomena for mixtures involving polymers are poorly understood. To overcome these difficulties, empirical models based on sampled data can be used instead, namely regression methods typical of machine learning field. They have the ability to learn the trends of a process without any knowledge about its particular physical and chemical laws. Therefore, they are useful for modeling complex processes, such as the free radical polymerization of methyl methacrylate achieved in a batch bulk process. The goal is to generate accurate predictions of monomer conversion, numerical average molecular weight and gravimetrical average molecular weight. This process is associated with non-linear gel and glass effects. For this purpose, an adaptive sampling technique is presented, which can select more samples around the regions where the values have a higher variation. Several machine learning methods are used for the modeling and their performance is compared: support vector machines, k-nearest neighbor, k-nearest neighbor and random forest, as well as an original algorithm, large margin nearest neighbor regression. The suggested method provides very good results compared to the other well-known regression algorithms.

Keywords: batch bulk methyl methacrylate polymerization, adaptive sampling, machine learning, large margin nearest neighbor regression

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Authors: Gareth Baxter

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We use a mathematical model of language change to examine two recently observed patterns of language change: one in which most speakers change gradually, following the mean of the community change, and one in which most individuals use predominantly one variant or another, and change rapidly if they change at all. The model is based on Croft’s Utterance Selection account of language change, which views language change as an evolutionary process, in which different variants (different ‘ways of saying the same thing’) compete for usage in a population of speakers. Language change occurs when a new variant replaces an older one as the convention within a given population. The present model extends a previous simpler model to include effects related to speaker aging and interspeaker variation in behaviour. The two patterns of individual change (one more centralized and the other more polarized) were recently observed in historical language changes, and it was further observed that slower changes were more associated with the centralized pattern, while quicker changes were more polarized. Our model suggests that the two patterns of change can be explained by different balances between the preference of speakers to use one variant over another and the degree of accommodation to (propensity to adapt towards) other speakers. The correlation with the rate of change appears naturally in our model, and results from the fact that both differential weighting of variants and the degree of accommodation affect the time for change to occur, while also determining the patterns of change. This work represents part of an ongoing effort to examine phenomena in language change through the use of mathematical models. This offers another way to evaluate qualitative explanations that cannot be practically tested (or cannot be tested at all) in a real-world, large-scale speech community.

Keywords: agent based modeling, cultural evolution, language change, social behavior modeling, social influence

Procedia PDF Downloads 222

Authors: Lila D. Sigdel, Chin J. Leo, Samanthika Liyanapathirana, Pan Hu, Minghao Lu

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Integral bridges are a class of bridges with integral or semi-integral abutments, designed without expansion joints in the bridge deck of the superstructure. Integral bridges are economical alternatives to conventional jointed bridges with lower maintenance costs and greater durability, thereby improving social and economic stability for the community. Integral bridges have also been proven to be effective in lowering the overall construction cost compared to the conventional type of bridges. However, there is significant uncertainty related to the design and analysis of integral bridges in response to cyclic thermal movements induced due to deck expansion and contraction. The cyclic thermal movements of the abutments increase the lateral earth pressures on the abutment and its foundation, leading to soil settlement and heaving of the backfill soil. Thus, the primary objective of this paper is to investigate the soil-abutment interaction under the cyclic translational movement of the abutment. Results from five experiments conducted to simulate different magnitudes of cyclic translational movements of abutments induced by thermal changes are presented, focusing on lateral earth pressure development at the abutment-soil interface. Test results show that the cycle number and magnitude of cyclic translational movements have significant effects on the escalation of lateral earth pressures. Experimentally observed earth pressure distributions behind the integral abutment were compared with the current design approaches, which shows that the most of the practices has under predicted the lateral earth pressure.

Keywords: integral bridge, cyclic thermal movement, lateral earth pressure, soil-structure interaction

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Authors: Selamawit Dires, Solomon Tesfamariam, Thomas Tannert

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Modern earthquake engineering and design encompass performance-based design philosophy. The main objective in performance-based design is to achieve a system performing precisely to meet the design objectives so to reduce unintended seismic risks and associated losses. Energy-based earthquake-resistant design is one of the design methodologies that can be implemented in performance-based earthquake engineering. In energy-based design, the seismic demand is usually described as the ratio of the hysteretic to input energy. Once the hysteretic energy is known as a percentage of the input energy, it is distributed among energy-dissipating components of a structure. The hysteretic to input energy ratio is highly dependent on the inherent damping of a structural system. In numerical analysis, damping can be modeled as stiffness-proportional, mass-proportional, or a linear combination of stiffness and mass. In this study, the effect of mathematical modeling of damping on the estimation of seismic energy demands is investigated by considering elastic-perfectly-plastic single-degree-of-freedom systems representing short to long period structures. Furthermore, the seismicity of Vancouver, Canada, is used in the nonlinear time history analysis. According to the preliminary results, the input energy demand is not sensitive to the type of damping models deployed. Hence, consistent results are achieved regardless of the damping models utilized in the numerical analyses. On the other hand, the hysteretic to input energy ratios vary significantly for the different damping models.

Keywords: damping, energy-based seismic design, hysteretic energy, input energy

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Authors: B. Mohammadi, A. Riazati, P. Soltan Sanjari, S. Azimbeik

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The ever-increasing development of civic demands on one hand; and the urban constrains for newly establish of infrastructures, on the other hand, perforce the engineering committees to apply non-conflicting methods in order to optimize the results. One of these optimized procedures to establish the main sewerage networks is the pipe jacking and micro-tunneling method. The raw information and researches are based on the experiments of the slurry micro-tunneling project of the Tehran main sewerage network that it has executed by the KAYSON co. The 4985 meters route of the mentioned project that is located nearby the Azadi square and the most vital arteries of Tehran is faced to 45% physical progress nowadays. The boring machine is made by the Herrenknecht and the diameter of the using concrete-polymer pipes are 1600 and 1800 millimeters. Placing and excavating several shafts on the ground and direct Tunnel boring between the axes of issued shafts is one of the requirements of the micro-tunneling. Considering the stream of the ground located shafts should care the hydraulic circumstances, civic conditions, site geography, traffic cautions and etc. The profile length has to convert to many shortened segment lines so the generated angle between the segments will be based in the manhole centers. Each segment line between two continues drive and receive the shaft, displays the jack location, driving angle and the path straight, thus, the diversity of issued angle causes the variety of jack positioning in the shaft. The jacking frame fixing conditions and it's associated dynamic load direction produces various patterns of Stress and Strain distribution and creating fatigues in the shaft wall and the soil surrounded the shaft. This pattern diversification makes the shaft wall transformed, unbalanced subsidence and alteration in the pipe jacking Stress Contour. This research is based on experiments of the Tehran's west sewerage plan and the numerical analysis the interaction of the soil around the shaft, shaft walls and the Jacking frame direction and finally, the suitable or unsuitable location of the pipe jacking shaft will be determined.

Keywords: underground structure, micro-tunneling, fatigue analysis, dynamic-soil–structure interaction, underground water, finite element analysis

Procedia PDF Downloads 305

Authors: Ping Li, Bing Feng, Junpu Zhao, Xudong Xie, Dangpeng Xu, Kuixing Zheng, Qihua Zhu, Xiaofeng Wei

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In laser driven inertial confinement fusion (ICF), the control of the temporal shape of the laser pulse is a key point to ensure an optimal interaction of laser-target. One of the main difficulties in controlling the temporal shape is the foot part control accuracy of high contrast pulse. Based on the analysis of pulse perturbation in the process of amplification and frequency conversion in high power lasers, an approach of beam spatio-temporal multiplexing is proposed to improve the control precision of high contrast pulse. In the approach, the foot and peak part of high contrast pulse are controlled independently, which propagate separately in the near field, and combine together in the far field to form the required pulse shape. For high contrast pulse, the beam area ratio of the two parts is optimized, and then beam fluence and intensity of the foot part are increased, which brings great convenience to the control of pulse. Meanwhile, the near field distribution of the two parts is also carefully designed to make sure their F-numbers are the same, which is another important parameter for laser-target interaction. The integrated calculation results show that for a pulse with a contrast of up to 500, the deviation of foot part can be improved from 20% to 5% by using beam spatio-temporal multiplexing approach with beam area ratio of 1/20, which is almost the same as that of peak part. The research results are expected to bring a breakthrough in power balance of high power laser facility.

Keywords: inertial confinement fusion, laser pulse control, beam spatio-temporal multiplexing, power balance

Procedia PDF Downloads 137